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  1. Sofware

    Automatic procedure for generating symmetry adapted wavefunctions

    Automatic detection of point groups as well as symmetrisation of molecular geometry and wavefunctions are useful tools in computational quantum chemistry. Algorithms for developing these tools as well as an im...

    Marcus Johansson and Valera Veryazov

    Journal of Cheminformatics 2017 9:8

    Published on: 2 February 2017

  2. Research article

    The power metric: a new statistically robust enrichment-type metric for virtual screening applications with early recovery capability

    A new metric for the evaluation of model performance in the field of virtual screening and quantitative structure–activity relationship applications is described. This metric has been termed the power metric a...

    Julio Cesar Dias Lopes, Fábio Mendes dos Santos, Andrelly Martins-José, Koen Augustyns and Hans De Winter

    Journal of Cheminformatics 2017 9:7

    Published on: 2 February 2017

  3. Database

    SkinSensDB: a curated database for skin sensitization assays

    Skin sensitization is an important toxicological endpoint for chemical hazard determination and safety assessment. Prediction of chemical skin sensitizer had traditionally relied on data from rodent models. Th...

    Chia-Chi Wang, Ying-Chi Lin, Shan-Shan Wang, Chieh Shih, Yi-Hui Lin and Chun-Wei Tung

    Journal of Cheminformatics 2017 9:5

    Published on: 31 January 2017

  4. Research article

    A metadata-driven approach to data repository design

    The design and use of a metadata-driven data repository for research data management is described. Metadata is collected automatically during the submission process whenever possible and is registered with Dat...

    Matthew J. Harvey, Andrew McLean and Henry S. Rzepa

    Journal of Cheminformatics 2017 9:4

    Published on: 24 January 2017

  5. Database

    S2RSLDB: a comprehensive manually curated, internet-accessible database of the sigma-2 receptor selective ligands

    Sigma (σ) receptors are accepted as a particular receptor class consisting of two subtypes: sigma-1 (σ1) and sigma-2 (σ2). The two receptor subtypes have specific drug actions, pharmacological profiles and molec...

    Giovanni Nastasi, Carla Miceli, Valeria Pittalà, Maria N. Modica, Orazio Prezzavento, Giuseppe Romeo, Antonio Rescifina, Agostino Marrazzo and Emanuele Amata

    Journal of Cheminformatics 2017 9:3

    Published on: 21 January 2017

  6. Database

    NPCARE: database of natural products and fractional extracts for cancer regulation

    Natural products have increasingly attracted much attention as a valuable resource for the development of anticancer medicines due to the structural novelty and good bioavailability. This necessitates a compr...

    Hwanho Choi, Sun Young Cho, Ho Jeong Pak, Youngsoo Kim, Jung-yun Choi, Yoon Jae Lee, Byung Hee Gong, Yeon Seok Kang, Taehoon Han, Geunbae Choi, Yeeun Cho, Soomin Lee, Dekwoo Ryoo and Hwangseo Park

    Journal of Cheminformatics 2017 9:2

    Published on: 5 January 2017

  7. Research article

    A novel descriptor based on atom-pair properties

    Molecular descriptors have been widely used to predict biological activities and physicochemical properties or to analyze chemical libraries on the basis of similarity. Although fingerprints and properties are...

    Masataka Kuroda

    Journal of Cheminformatics 2017 9:1

    Published on: 5 January 2017

  8. Research article

    osFP: a web server for predicting the oligomeric states of fluorescent proteins

    Currently, monomeric fluorescent proteins (FP) are ideal markers for protein tagging. The prediction of oligomeric states is helpful for enhancing live biomedical imaging. Computational prediction of FP oligom...

    Saw Simeon, Watshara Shoombuatong, Nuttapat Anuwongcharoen, Likit Preeyanon, Virapong Prachayasittikul, Jarl E. S. Wikberg and Chanin Nantasenamat

    Journal of Cheminformatics 2016 8:72

    Published on: 20 December 2016

  9. Research article

    Mapping the 3D structures of small molecule binding sites

    Analysis of the 3D structures of protein–ligand binding sites can provide valuable insights for drug discovery. Binding site comparison (BSC) studies can be employed to elucidate the function of orphan protein...

    Joshua Meyers, Nathan Brown and Julian Blagg

    Journal of Cheminformatics 2016 8:70

    Published on: 6 December 2016

  10. Methodology

    A novel applicability domain technique for mapping predictive reliability across the chemical space of a QSAR: reliability-density neighbourhood

    The ability to define the regions of chemical space where a predictive model can be safely used is a necessary condition to assure the reliability of new predictions. This implies that reliability must be dete...

    Natália Aniceto, Alex A. Freitas, Andreas Bender and Taravat Ghafourian

    Journal of Cheminformatics 2016 8:69

    Published on: 3 December 2016

  11. Research Article

    Prediction of reacting atoms for the major biotransformation reactions of organic xenobiotics

    The knowledge of drug metabolite structures is essential at the early stage of drug discovery to understand the potential liabilities and risks connected with biotransformation. The determination of the site o...

    Anastasia V. Rudik, Alexander V. Dmitriev, Alexey A. Lagunin, Dmitry A. Filimonov and Vladimir V. Poroikov

    Journal of Cheminformatics 2016 8:68

    Published on: 28 November 2016

  12. Methodology

    Programmatic conversion of crystal structures into 3D printable files using Jmol

    Three-dimensional (3D) printed crystal structures are useful for chemistry teaching and research. Current manual methods of converting crystal structures into 3D printable files are time-consuming and tedious....

    Vincent F. Scalfani, Antony J. Williams, Valery Tkachenko, Karen Karapetyan, Alexey Pshenichnov, Robert M. Hanson, Jahred M. Liddie and Jason E. Bara

    Journal of Cheminformatics 2016 8:66

    Published on: 23 November 2016

  13. Software

    LA-iMageS: a software for elemental distribution bioimaging using LA–ICP–MS data

    The spatial distribution of chemical elements in different types of samples is an important field in several research areas such as biology, paleontology or biomedicine, among others. Elemental distribution im...

    Hugo López-Fernández, Gustavo de S. Pessôa, Marco A. Z. Arruda, José L. Capelo-Martínez, Florentino Fdez-Riverola, Daniel Glez-Peña and Miguel Reboiro-Jato

    Journal of Cheminformatics 2016 8:65

    Published on: 18 November 2016

  14. Methodology

    Consensus Diversity Plots: a global diversity analysis of chemical libraries

    Measuring the structural diversity of compound databases is relevant in drug discovery and many other areas of chemistry. Since molecular diversity depends on molecular representation, comprehensive chemoinfor...

    Mariana González-Medina, Fernando D. Prieto-Martínez, John R. Owen and José L. Medina-Franco

    Journal of Cheminformatics 2016 8:63

    Published on: 10 November 2016

  15. Research article

    DRABAL: novel method to mine large high-throughput screening assays using Bayesian active learning

    Mining high-throughput screening (HTS) assays is key for enhancing decisions in the area of drug repositioning and drug discovery. However, many challenges are encountered in the process of developing suitabl...

    Othman Soufan, Wail Ba-Alawi, Moataz Afeef, Magbubah Essack, Panos Kalnis and Vladimir B. Bajic

    Journal of Cheminformatics 2016 8:64

    Published on: 10 November 2016

  16. Software

    ClassyFire: automated chemical classification with a comprehensive, computable taxonomy

    Scientists have long been driven by the desire to describe, organize, classify, and compare objects using taxonomies and/or ontologies. In contrast to biology, geology, and many other scientific disciplines, t...

    Yannick Djoumbou Feunang, Roman Eisner, Craig Knox, Leonid Chepelev, Janna Hastings, Gareth Owen, Eoin Fahy, Christoph Steinbeck, Shankar Subramanian, Evan Bolton, Russell Greiner and David S. Wishart

    Journal of Cheminformatics 2016 8:61

    Published on: 4 November 2016

  17. Research article

    Recognizing chemicals in patents: a comparative analysis

    Recently, methods for Chemical Named Entity Recognition (NER) have gained substantial interest, driven by the need for automatically analyzing todays ever growing collections of biomedical text. Chemical NER f...

    Maryam Habibi, David Luis Wiegandt, Florian Schmedding and Ulf Leser

    Journal of Cheminformatics 2016 8:59

    Published on: 28 October 2016

  18. Methodology

    Multi-level meta-workflows: new concept for regularly occurring tasks in quantum chemistry

    In Quantum Chemistry, many tasks are reoccurring frequently, e.g. geometry optimizations, benchmarking series etc. Here, workflows can help to reduce the time of manual job definition and output extraction. T...

    Junaid Arshad, Alexander Hoffmann, Sandra Gesing, Richard Grunzke, Jens Krüger, Tamas Kiss, Sonja Herres-Pawlis and Gabor Terstyanszky

    Journal of Cheminformatics 2016 8:58

    Published on: 20 October 2016

  19. Research article

    Benchmark of four popular virtual screening programs: construction of the active/decoy dataset remains a major determinant of measured performance

    In a structure-based virtual screening, the choice of the docking program is essential for the success of a hit identification. Benchmarks are meant to help in guiding this choice, especially when undertaken ...

    Ludovic Chaput, Juan Martinez-Sanz, Nicolas Saettel and Liliane Mouawad

    Journal of Cheminformatics 2016 8:56

    Published on: 17 October 2016

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